geva.summarize: Summarizes the GEVAInput

Description Usage Arguments Details Value See Also Examples

View source: R/summarization.R

Description

Performs the summarization step by calculating the central points and variation estimates of logFC values from the input data.

Usage

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geva.summarize(
  ginput,
  summary.method = options.summary,
  variation.method = options.variation,
  ...
)

options.summary
# c("mean", "median")

options.variation
# c("sd", "var", "mad")

Arguments

ginput

a GEVAInput object

summary.method

single character, method used to calculate the central (summarized) logFC values

variation.method

single character, method used to calculate the distribution degree (variation) of the logFC values

...

additional arguments. Accepts verbose (logical, default is TRUE) to enable or disable printing the current progress

Details

The options.summary refer to the available operations to calculate central logFC values (mean or median), whereas options.variation presents three functions to calculate logFC variation (sd: Standard Deviation; var: Variance; and mad: Median Absolute Deviation). Moreover, all those operations include a weighted counterpart applied using the weights table from the GEVAInput object.

Value

A GEVASummary object

See Also

base::mean(), stats::median()

stats::var(), stats::sd(), stats::mad()

Examples

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## Summarization of a randomly generated input
ginput <- geva.ideal.example()     # Generates a random input example
gsummary <- geva.summarize(ginput) # Summarizes with the default parameters
plot(gsummary)                     # Plots the summarized data

nunesijg/geva documentation built on March 12, 2021, 3:58 p.m.